Abstract

While it is clear that bacteriophages, the viruses that infect bacteria, abound in all bacterial communities, their role in the ecology of these communities remains poorly understood. In particular, in the gut microbiota, it is unknown whether phage regulate the population densities of their host bacteria and influence the composition of this ecosystem. In the intestine of mice, usually only a fraction of susceptible bacteria are killed by phage, suggesting thatphysiology complicates phage multiplication in this environment.

We studied the population dynamics of phage-bacteria interactions in gnotoxenic mice, i. e. mice colonized with only one or two bacterial species. With Escherichia coli, we showed that lambda phage is responsible of more bacterial mortality than what could have been expected from in vitro estimation of phage-bacteria interactions. With a dominant gut microbiota species, Roseburia intestinalis, we showed that phage infection killed the majority of susceptible bacteria in a few days. Yet, resistant bacteria also appeared very rapidly, mainly through new spacer acquisition in a CRISPR array, limiting bacterial mortality, and leading to an equilibrium of phage and bacterial populations. Altogether, these results suggests that phage are important killers of bacteria in the gut microbiota, and drive its evolution and diversification.